Submitted to Ecology Letters, Evolution or Evolution Letters – well let’s see what we find!
Affiliations: 1Department of Bioscience, Durham University, Stockton Rd., Durham DH1 3LE, UK. 2University of Sao Paulo, xxxxx. 3Systematic Botany and Mycology, Department of Biology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany.
Correspondence: *guillaume.chomicki@durham.ac.uk
The results below follow the same rationale as the ones from the main document. However, in the cases below all analyses use the plant traits already accounted for climatic effects by using the residuals from the regressions between each trait and the first three Principal Components of the climatic variables obtained from BioClim (REF).
here::i_am("manuscript/chomicki_et_al_climpc.Rmd")
source(here::here("R/tree_plots.R"))
library("knitr")
library("RColorBrewer")
library("kableExtra")
# load("../output/first_analysis.RData")
knitr::opts_chunk$set(fig.pos = "h", out.extra = "")
# source("../R/ouwie_summary_mcc.R")
pars.table.pc1 <- read.csv(here::here("output/fullpar_table_climpc1.csv"))
pars.table.pc1$trait <- c("Stem Area", "Leaf Area", "Corola Length", "Petiole Length", "Hole Diameter")[match(pars.table.pc1$trait, c("stemarea", "leafarea", "corleng", "petleng", "holediam"))]
pars.table.pc2 <- read.csv(here::here("output/fullpar_table_climpc2.csv"))
pars.table.pc2$trait <- c("Stem Area", "Leaf Area", "Corola Length", "Petiole Length", "Hole Diameter")[match(pars.table.pc2$trait, c("stemarea", "leafarea", "corleng", "petleng", "holediam"))]
pars.table.pc3 <- read.csv(here::here("output/fullpar_table_climpc3.csv"))
pars.table.pc3$trait <- c("Stem Area", "Leaf Area", "Corola Length", "Petiole Length", "Hole Diameter")[match(pars.table.pc3$trait, c("stemarea", "leafarea", "corleng", "petleng", "holediam"))]
colors <- setNames(brewer.pal(4, "Set1"), 1:4)
sig.formatter <- function(x){cell_spec(x, format = "latex", bold = ifelse(x > 75, TRUE, FALSE), background = if(x >= 90){"red"} else if(x < 90 & x >= 50){"yellow"})}
The following figure represents the summary of 1000 stochastic maps for each discrete trait, that were summarized for each node.
Lastly, we fitted all 7 models of leaf area evolution to 10 sampled evolutionary histories of mutualistic strategy. Due to the elevated number of variables and models, we opted to use a model averaging approach by calculating the weighted average of parameter values. The final value of each parameter was calculated by multiplying the estimated value for a given parameter in a given model by the Akaike weight of the given model. Thus, we need not resort to any arbitrary criterium (such as \(\delta\)AIC > 2) and can evaluate the dynamics solely based on the parameter values.
All plots below were filtered to exclude parameter values that were larger than -10 (\(e^-10\)) and smaller than 10 (\(e^10\)), on the justification of representing bad fitting or unreasonable biological meaning.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Appendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Appendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Appendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Archendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Archendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Archendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Domgrowendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Domgrowendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Domgrowendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Leafstrucendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Leafstrucendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Leafstrucendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Matsysendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Matsysendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Matsysendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Rewardendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Rewardendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Rewardendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Strategyendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Strategyendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Strategyendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Wartsendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Wartsendage.
Distribution of Theta (A), Alpha (B) and Sigma (C) values for the OU-based models for each continuous trait in association with different states of Wartsendage.